Fungus Fuels Tree GrowthPoplar is the fastest growing hardwood tree in the western United States, making it an energy feedstock of particular interest to the U.S. Department of Energy (DOE). The fungus is almost always found among and within poplar trees, and in an effort to understand its influence on the plant, a team of scientists studied what happens to the tree’s physical traits and gene expression when the fungus is present.

Better Genome Editing for BioenergyCRISPR-Cas9 is a powerful, high-throughput gene-editing tool that can help scientists engineer organisms for bioenergy applications. Cas9 needs guide RNA to lead it to the correct sequence to snip—but not all guides are effective. Researchers created a set of guide RNAs that were effective against 94 percent of the genes in a lipid-prolific yeast.

Cultivating Symbiotic Antarctic MicrobesIn the Proceedings of the National Academy of Sciences, researchers employed multiple microbiology and ‘omics techniques to experimentally determine that Nanohaloarchaeota are not free-living archaea but rather symbionts.

Methane Flux in the AmazonWetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

Insights into Functional Diversity in NeurosporaThis proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

Improving the Cacao Genome and PhytozomeAn updated reference genome for Theobroma cacao Matina 1-6 has now been completed and released by HudsonAlpha scientists, with the help of Mars Wrigley funding. The annotated genome has been updated to a high quality modern standard and includes RNA-seq data. The improved genome is available for comparative purposes on the latest version of the JGI plant portal Phytozome (phytozome-next.JGI.doe.gov).

Mining IMG/M for CRISPR-Associated ProteinsResearchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

What Happens Underground Influences Global Nutrient CyclesThrough the Facilities Integrating Collaborations for User Science (FICUS) program, the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (JGI) have selected 11 proposals for support from 53 received through a joint research call.

CSP Functional Genomics Call OngoingThe CSP Functional Genomics call is to enable users to perform state-of-the-art functional genomics research and to help them translate genomic information into biological function. Proposals submitted by January 31, 2019 will be part of the next review.

Learning to LookUsing machine learning, JGI researchers combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes.

JGI Early Career Researchers in mSystems Special IssueJGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like. In one article, Rex Malmstrom and Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental sample. In a separate article, Simon Roux makes a pitch for readers to get involved in the developing field of virus ecogenomics.

Hidden Giants in Forest SoilsIn Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.

Uncovered: 1000 New Microbial Genomes

Potential biotech applications seen with release of 1,003 reference bacterial and archaeal genomes.

The release of 1,003 phylogenetically diverse bacterial and archaeal reference genomes, the single largest release to date, is part of the DOE JGI’s Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative. (Zosia Rostomian, Berkeley Lab Creative Services.)

The number of microbes in a handful of soil exceeds the number of stars in the Milky Way galaxy, but researchers know less about what’s on Earth because they have only recently had the tools to deeply explore what is just underfoot. Now scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, have taken a decisive step forward in uncovering the planet’s microbial diversity. In a paper published June 12, 2017 in Nature Biotechnology, DOE JGI’s Prokaryotic Super Program head Nikos Kyrpides and his team of researchers report the release of 1,003 phylogenetically diverse bacterial and archaeal reference genomes—the single largest release to date.

“Bacteria and archaea comprise the largest amount of biodiversity of free-living organisms on Earth,” said Kyrpides, senior author of the paper. “They have already conquered every environment on the planet, so they have found ways to survive under the harshest of conditions with different enzymes and with different biochemistry.”

The U.S. Department of Energy is interested in learning more about this biodiversity because microbes play important roles in regulating Earth’s biogeochemical cycles—processes that govern nutrient circulation in terrestrial and marine environments, for example. Uncovering the functions of genes, enzymes and metabolic pathways through genome sequencing and analysis has wide applications in the fields of bioenergy, biomedicine, agriculture and environmental sciences.

New Functions, New Applications

The effort is part of the DOE JGI’s Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative that aims to sequence thousands of bacterial and archaeal genomes to fill in unexplored branches of the tree of life. “In addition to identifying over half a million new protein families, this effort has more than doubled the coverage of phylogenetic diversity of all type strains with genome sequences”, said Supratim Mukherjee, a DOE JGI computational biologist and co-first author of the paper.

Since a great portion of research in microbial genomics has been focused on human pathogens or biotechnological work horses, GEBA is the main effort worldwide attempting to address the phylogenetic coverage knowledge gap by sequencing a diverse set of cultured but poorly characterized microbial type strains. “It was recognized that we weren’t sampling many parts of the tree of life,” said Rekha Seshadri, a DOE JGI computational biologist and co-first author of the paper. “And if we sampled some of those parts of the tree, we’d discover new functions, which could be an important resource for new applications.”

The release of these genomes is the culmination of almost a decade’s worth of work, with the first 56 GEBA genomes published in 2009. The microorganisms were isolated from environments ranging from sea water and soil, to plants, and to cow rumen and termite guts. Genome sequencing and analysis was done at the DOE JGI through the Community Science Program, and the 1,003 genomes are publicly available through the Integrated Microbial Genomes with Microbiomes (IMG/M) system, with all associated metadata in compliance with the Genomics Standards Consortium available through the Genomes OnLine Database. In fact, all these genomes were publicly released immediately after sequencing to maximize their use by the larger scientific community, in accordance with the DOE JGI’s practice of immediate data release, said co-author Tanja Woyke, head of the DOE JGI Microbial Genomics Program, who overviewed the sequencing of the project.

With the release of high quality genomic information from the 1,003 reference genomes, DOE JGI is providing a wealth of new sequences that will be invaluable to scientists interested in experiments such as characterizing biotechnologically relevant secondary metabolites or studying enzymes that work under specific conditions, Seshadri said. And because Kyrpides’ research team sequenced type strains that are readily available from culture collections, scientists can perform follow-up experiments with them in the lab, she added.

“The partnership with culture collection centers such as the Leibniz Institute DSMZ in Germany and the ATCC Global Bioresource Center in the U.S., was critical in accomplishing this endeavor,” said Kyrpides.

Though it’s evident that bacteria can jumpstart innovations in biotechnology—such as the species Streptococcus pyogenes, which produces the Cas9 protein that functions as the “scissors” in the breakthrough CRISPR-Cas9 gene editing tool—scientists have only just begun to uncover the hidden potential that exists within the wide genetic diversity of bacterial and archaeal phyla.

A Reference Framework to Anchor Data

Jonathan Eisen, a microbiologist at the University of California, Davis who initiated the GEBA project at the DOE JGI in 2007 with Kyrpides and Phil Hugenholtz, and Hans-Peter Klenk at the Leibniz Institute DSMZ, believes that the paper reinforces that having a goal to achieve phylogenetic diversity is a more useful approach than random selection when choosing microbial organisms for sequencing.

He said filling out the tree of life will provide researchers with a reference framework with which to understand their own results. “It’s incredibly helpful for interpreting environmental data. For example, if you go and find a fossil bed somewhere and find tons of bones, but if no one had ever assembled skeletons before, it’d be useless,” Eisen said. “But with an assembled skeleton to use as a reference, “you can say ‘this looks like a mammal’. The same is true with metagenomic data—if you have reference genomes from across the tree [of life], you can anchor environmental data much more accurately.”

“At a time when we are witnessing the public databases being flooded by an infusion of low or questionable quality, highly fragmented and chimeric or contaminated genomes, the significance of genomes from the type strains as invaluable taxonomic signposts cannot be overstated,” Kyrpides said.

Collaborators on this work included researchers a the Leibniz Institute DSMZ in Germany, the University of Georgia, Michigan State University, the University of Queensland in Australia and Newcastle University in the United Kingdom.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.